Methods and tools for plant pathogen assessment

Abstract

Described herein are methods, products and tools for plant pathogen assessment and management. Also described are collections, kits and packages comprising reagents (e.g. oligonucleotides) and uses thereof, for example for plant pathogen assessment. In an embodiment, the pathogen is a Phytophthora pathogen, in a further embodiment Phytophthora sojae. In an embodiment the plant is soybean.

1 . A method for assessing whether a  Phytophthora  pathogen is virulent or avirulent, comprising:
 (a) determining, in a sample comprising  Phytophthora  nucleic acid, the presence or absence of one or more Avr gene variations in the  Phytophthora  nucleic acid; and   (b) determining whether the  Phytophthora  pathogen is virulent or avirulent on the basis of the presence or absence of the one or more variations.   
     
     
         2 . The method of  claim 1 , wherein the one or more variations are comprised in one or more of Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a and Avr6 or a flanking region thereof. 
     
     
         3 . The method of  claim 1  or  2 , wherein the one or more variations are each independently a substitution, deletion or insertion of one or more nucleotides. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein the variations are one or more indels and/or SNPs corresponding to one or more indels and/or SNPs set forth in  FIGS. 1  (Avr1a),  3  (Avr1b),  5  (Avr1c),  7  (Avr1c),  9  (Avr1k),  11  (Avr3a) and/or  12  (Avr6),  16 - 23  and/or Table 4 and/or 5. 
     
     
         6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein the presence or absence of the one or more variations is determined using an amplification method. 
     
     
         8 - 9 . (canceled) 
     
     
         10 . The method of  claim 7 , wherein the amplification is carried out as one or more multiplex amplifications for determination of the presence or absence of two or more variations in each amplification reaction. 
     
     
         11 . The method of  claim 10 , wherein the one or more multiplex amplifications comprises or consists of two multiplex amplifications. 
     
     
         12 . The method of  claim 11 , wherein the two multiplex amplifications comprise (a) a first multiplex amplification to determine the presence or absence of one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1a shown in  FIGS. 1, 16 and/or 23 , and/or Table 4 and/or 5 one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1b, Avr1d, Avr1k, Avr3a and Avr6 shown in  FIGS. 3, 7, 9, 11, 13 and/or 17 and 19-23 , and/or Table 4 and/or 5; and (b) a second amplification to determine the presence or absence of one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1c shown in  FIGS. 5, 18 , and/or  23 , and/or Table 4 and/or 5. 
     
     
         13 - 16 . (canceled) 
     
     
         17 . The method of  claim 1 , wherein the  Phytophthora  pathogen is  Phytophthora sojae.    
     
     
         18 . A method for assessing risk of  Phytophthora  pathogen infection of a soybean plant:
 (a) assessing, in a sample obtained from the plant, the soil, the water, the seeds, the air, or any culture containing one or several isolates of  Phytophthora  pathogen, whether the sample comprises a virulent or avirulent  Phytophthora  pathogen using the method of  claim 1 ; and   (b) assessing the risk of  Phytophthora  pathogen infection of the soybean plant on the basis of the assessment made in (a), wherein the presence of a virulent  Phytophthora  pathogen in the sample is indicative of an elevated risk of  Phytophthora  pathogen infection of the soybean plant.   
     
     
         19 . (canceled) 
     
     
         20 . A method for selecting a soybean cultivar for planting in an agricultural area, comprising:
 (a) assessing, in a sample obtained from the plant, the soil, the water, the seeds, the air, or any culture containing one or several isolates of  Phytophthora  pathogen, whether the sample comprises a virulent or avirulent  Phytophthora  pathogen using the method of  claim 1 ;   (b) if the sample comprises a virulent  Phytophthora  pathogen, selecting a soybean cultivar comprising one or more resistances (Rps) genes that confer resistance to the one or more Avr genes identified in the sample that confer virulence, for planting in the agricultural area.   
     
     
         21 . A collection, kit or package comprising one or more oligonucleotides for determining the presence or absence of one or more Avr gene variations in the nucleic acid of a  Phytophthora  pathogen. 
     
     
         22 . The collection, kit or package of  claim 21 , wherein the one or more variations are comprised in one or more of Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a and Avr6 or a flanking region thereof. 
     
     
         23 . The collection, kit or package of  claim 21  or  22 , wherein the one or more variations are each independently a substitution, deletion or insertion of one or more nucleotides. 
     
     
         24 . (canceled) 
     
     
         25 . The collection, kit or package of  claim 21 , wherein the variations are one or more indels and/or SNPs corresponding to one or more indels and/or SNPs set forth in  FIGS. 1  (Avr1a),  3  (Avr1b),  5  (Avr1c),  7  (Avr1d),  9  (Avr1k),  11  (Avr3a) and/or  12  (Avr6),  16 - 23  and/or Table 4 and/or 5. 
     
     
         26 . (canceled) 
     
     
         27 . The collection, kit or package of  claim 21 , wherein the presence or absence of the one or more variations is determined using an amplification method. 
     
     
         28 - 29 . (canceled) 
     
     
         30 . The collection, kit or package of  claim 27 , wherein the one or more oligonucleotides are for use in one or more multiplex amplifications for determination of the presence or absence of two or more variations in each amplification reaction. 
     
     
         31 . The collection, kit or package of  claim 30 , wherein the one or more multiplex amplifications comprises or consists of two multiplex amplifications. 
     
     
         32 . The collection, kit or package of  claim 31 , wherein the two multiplex amplifications comprise (a) a first multiplex amplification to determine the presence or absence of one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1a shown in  FIGS. 1, 16 and/or 23 , and/or Table 4 and/or 5 one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1b, Avr1d, Avr1k, Avr3a and Avr6 shown in  FIGS. 3, 7, 9, 11, 13 and/or 17 and 19-23 , and/or Table 4 and/or 5; and (b) a second amplification to determine the presence or absence of one or more indels and/or SNPs corresponding to one or more indels and/or SNPs in Avr1c shown in  FIGS. 5, 18 , and/or  23 , and/or Table 4 and/or 5. 
     
     
         33 - 36 . (canceled) 
     
     
         37 . The collection, kit or package of  claim 21 , wherein the  Phytophthora  pathogen is  Phytophthora sojae.    
     
     
         38 . (canceled)